Associative role of HLA‐DRB1 SNP genotypes as risk factors for susceptibility and severity of rheumatoid arthritis: A North‐east Indian population‐based study

Rheumatoid arthritis (RA) is a complex, multifactorial, systemic autoimmune disease. Reports are suggestive of the role of HLA especially HLA‐DRB1 alterations in RA pathogenesis. Existing data involving different geographical populations on the role of alterations in specific locus of HLA‐DRB1 in RA susceptibility and severity are equivocal, with no data available from ethnically distinct North‐east Indian population, where RA cases are alarmingly increasing. This study aimed to evaluate the association of HLA‐DRB1 gene SNPs (rs13192471, rs660895 and rs6457617) with susceptibility and severity of RA in an ethnically distinct North‐east Indian population. Whole blood was collected from clinically characterized RA cases (satisfying the American College of Rheumatology 1987 criteria) (n = 123) and community‐based age and sex‐matched healthy controls (n = 156) with informed consent. The HLA‐DRB1 SNP analysis was performed for all the RA and control cases using ARMS‐PCR using case and control genomic DNA as template. Statistical analysis was performed by SPSSv13.0 software. The HLA‐DRB1 rs660895 showed both wild (AA) and heterozygote (AG) genotype but the heterozygote allele was found to be associated with reduced risk of RA compared to controls [OR = 0.531, p = .024]. The difference in distribution of rs6457617 polymorphism between RA and control cases was comparable [OR = 0.525, p = .079]. Significantly higher distribution of variant rs13192471 genotype was observed in RA cases (69.92%) compared to controls (46.75%) (p < .001) and was associated with increased risk of susceptibility to RA [OR = 2.576, p < .001] compared to controls, as well as progression to severity in RA cases [OR = 2.404, p = .048]. Combinatorially also, the presence of rs13192471 variant genotype was associated with increased risk of RA susceptibility [OR = 8.267, p = .026] and RA severity [OR = 3.647, p = .280]. Alterations in HLA‐DRB1 are associated with RA susceptibility. HLA‐DRB1 rs13192471 SNP plays a critical role in RA susceptibility and severity in North‐east Indian cases and has prognostic significance in RA.     

Association of PTPN22 rs2476601 and EGFR rs17337023 Gene polymorphisms and rheumatoid arthritis in Zahedan,Southeast Iran

In this study we aimed to evaluate the possible association of PTPN22 rs2476601 as well as epidermal growth factor receptor (EGFR) rs17337023 gene polymorphism and rheumatoid arthritis (RA) in a sample of Iranian population. This case‐control study was performed on 120 patients with RA and 120 healthy subjects. Genomic DNA was extracted from whole blood and PTPN22 rs2476601 and EGFR rs17337023 polymorphisms were determined using tetra amplification refractory mutation system–polymerase chain reaction (T‐ARMS‐PCR). The results showed that PTPN22 rs2476601 CT genotype as well as rs2476601 T allele was a risk factor for susceptibility to RA (OR=5.89 95%CI = 1.78–19.48, P = 0.004 and OR = 4.78, 95%CI = 1.59–14.35, P = 0.003, respectively). We also found that EGFR rs17337023 AT and rs17337023 TT genotypes were risk factor for susceptibility to RA (OR = 9.94 95%CI = 3.65–26.73, P < 0.001 and OR = 3.66, 95%CI = 1.46–9.15, P = 0.005, respectively). In addition the EGFR rs17337023 T allele was a risk for predisposition to RA (OR = 1.56, 95%CI=1.06‐2.30, P = 0.030). In conclusion, we found an association between PTPN22 rs2476601 and EGFR rs17337023 polymorphisms and the risk of RA in a sample of Iranian population.     

Human leucocyte antigen but not KIR alleles and haplotypes associated with chronic HCV infection in a Chinese Han population

The host immune system plays a key role in the elimination of infected cells which depend on killer‐cell immunoglobulin‐like receptors (KIR), human leucocyte antigen (HLA) class I molecules and their combinations. To evaluate the roles of HLAclass I, KIR genes and their combination in Chronic hepatitis C virus (HCV) infection (CHC), a total of 301 CHCs and 239 controls in a Chinese Han population were included for HLA and KIR genotyping using next‐generation sequencing and multiplex PCR sequence‐specific priming, respectively. The allele frequency of HLA‐C*08:01 was significantly higher in the CHCs than that of the controls (0.088 vs. 0.040, OR = 2.332, 95%CI: 1.361–3.996, p = 0.022), while the frequencies of B*13:01 (0.032 vs. 0.084, OR = 0.357, 95%CI: 0.204–0.625, p = 0.009) and C*08:04 (0.008 vs. 0.038, OR = 0.214, 95%CI: 0.079–0.581, p = 0.022) were significantly lower in the CHCs. The frequencies of haplotype A*11:01‐C*08:01 were higher in the CHCs (0.058 vs. 0.019, OR = 3.096, 95%CI: 1.486–6.452, p = 0.026), while haplotype B*13:01‐C*03:04 were lower in the CHCs compared to the controls (0.028 vs. 0.071, OR = 0.377, 95%CI: 0.207–0.685, p = 0.012). No association of CHC with KIR genes, genotypes, or haplotypes, as well as HLA/KIR combinations was observed. Our results indicated that HLA‐C*08:01 was a risk factor for CHC, while HLA‐C*08:04 and HLA‐B*13:01 were protective factors against CHC. Haplotypes HLA‐A*11:01‐C*08:01 could increase susceptibility to CHC, while HLA‐B*13:01‐C*03:04 could be protective against CHC in the Chinese Han population.     

Polymorphisms in IL‐1A are associated with endometrial cancer susceptibility among Chinese Han population: A case–control study

Endometrial cancer (EC) is one of the most common malignant tumours of the female genital tract, and it has become a serious malignant disease of the female genital tract in China. Existing researches have revealed the association between polymorphisms of IL‐1A and several gynaecological diseases. In this research, we analysed the association between IL‐1A gene polymorphisms and endometrial cancer susceptibility in Chinese female population. A total of 81 patients and 198 healthy people were selected. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression. Genetic models and analyses showed that IL‐1A rs3783550 TT and rs3783546 CC increased the risk of endometrial cancer under the recessive model, respectively (rs3783550: OR = 2.80, 95%CI: 1.32–5.92, p = .008; rs3783546: OR = 2.79, 95%CI: 1.32–5.89, p = .008). In the recessive model, we also found that both IL‐1A rs1609682 and IL‐1A rs3783521 increased the risk of endometrial cancer, respectively (rs1609682: OR = 2.79, 95%CI: 1.32–5.89, p = .0081; rs3783521: OR = 2.80, 95%CI: 1.32–5.92, p = .008). Haplotype analysis was performed that did not reveal any significant results. In summary, IL‐1A rs3783550, rs3783546, rs1609682 and rs3783521 polymorphisms may be associated with an increased risk of endometrial cancer in Chinese female populations.     

Cadherin 5 is Regulated by Corticosteroids and Associated with Central Serous Chorioretinopathy

Central serous chorioretinopathy (CSC) is characterized by leakage of fluid from the choroid into the subretinal space and, consequently, loss of central vision. The disease is triggered by endogenous and exogenous corticosteroid imbalance and psychosocial stress and is much more prevalent in men. We studied the association of genetic variation in 44 genes from stress response and corticosteroid metabolism pathways with the CSC phenotype in two independent cohorts of 400 CSC cases and 1,400 matched controls. The expression of cadherin 5 (CDH5), the major cell–cell adhesion molecule in vascular endothelium, was downregulated by corticosteroids which may increase permeability of choroidal vasculature, leading to fluid leakage under the retina. We found a significant association of four common CDH5 SNPs with CSC in male patients in both cohorts. Two common intronic variants, rs7499886:A>G and rs1073584:C>T, exhibit strongly significant associations with CSC; P = 0.00012; odds ratio (OR) = 1.5; 95%CI [1.2;1.8], and P = 0.0014; OR = 0.70; 95%CI [0.57;0.87], respectively. A common haplotype was present in 25.4% male CSC cases and in 35.8% controls (P = 0.0002; OR = 0.61, 95% CI [0.47–0.79]). We propose that genetically predetermined variation in CDH5, when combined with triggering events such as corticosteroid treatment or severe hormonal imbalance, underlie a substantial proportion of CSC in the male population.     

HLA‐DRB1 gene polymorphisms and its associations with rheumatoid arthritis in Chinese Han women of Shaanxi province,northwest of China

Rheumatoid arthritis (RA) is a common chronic autoimmune disease characterized by symmetric polyarthritis. This study was designed to investigate the associations between HLA‐DRB1 gene polymorphisms and RA in the Chinese Han population of Shaanxi province, northwest of China. In total, we identified 31 high‐resolution HLA‐DRB1 alleles in 109 patients with RA. Compared with the controls, the AF of HLA‐DRB1*04:05 (P = 0.000, Pc = 0.007, OR = 3.462, 95%CI: 1.749–6.852) was significantly higher in patients with RA. In addition, the patients with RA had higher allele frequency (AF) of the HLA‐DRB1*04:03 (P = 0.030, Pc = NS, OR = 4.737, 95%CI: 1.012–22.180); DRB1*04:06 (P = 0.018, Pc = NS, OR = 5.288, 95%CI: 1.145–24.422) and the shared epitope (SE) alleles (P = 0.004, Pc = NS, OR = 2.166, 95%CI: 1.279–3.667), respectively. Moreover, positive possibilities of RF and anti‐CCP were significant higher in SE‐positive patients compared to SR‐negative patients (OR = 4.787, 95%CI: 1.101–20.824; OR = 3.775, 95%CI: 1.106–12.876, respectively). Our results indicated that HLA‐DRB1*04:05, *04:03, *04:06 and SE alleles might be susceptibility allele for RA in Chinese Han population of Shaanxi province, northwest of China.     

Association of complement factor B allotypes and serum biomarkers in rheumatoid arthritis patients and their relatives

The aim of the study was to investigate the allotypic variability of complement factor B (BF) in patients and relatives with rheumatoid arthritis (RA) and its association with serological biomarkers and clinical features of the disease. BF allotypes were determined by high‐voltage agarose gel electrophoresis in serum samples of 180 patients with RA, 198 relatives and 98 controls from Southern Brazil. Anticyclic citrullinated peptide (anti‐CCP), antimutated citrullinated vimentin (anti‐MCV) and IgA‐rheumatoid factor (RF) were determined by ELISA and IgM‐RF by latex agglutination in all samples. No significant differences were found in the allotypic variants of BF between patients with RA, relatives and controls, nor associations with gender and age of RA onset. BF*S07 allotype was significantly associated with extra‐articular manifestations (EAMs; Secondary Sjögren Syndrome, pneumonitis, rheumatoid nodules) in patients with RA (P = 0.02; OR = 6.62). Patients with phenotype BF F had lower positivity for anti‐MCV biomarker (P = 0.02; OR = 0.22) and those with allotype BF*S had higher prevalence of this autoantibody (P = 0.02; OR = 3.77). An increased frequency of RF‐IgA was detected in relatives of patients with RA with BF FS07 phenotype (P = 0.02; OR = 7.78). Complement BF variability did not influence the development of RA in the studied patients, but BF variants may act as markers of disease prognosis, such as development of EAMs, corroborating with the role of the alternative pathway in the pathogenesis of RA.     

Dominant-negative pathogenic variant BRIP1 c.1045G>C is a high-risk allele for non-mucinous epithelial ovarian cancer: A case-control study

BRIP1 is a moderate susceptibility epithelial ovarian cancer (EOC) gene. Having identified the BRIP1 c.1045G>C missense variant in a number of families with EOC, we aimed to investigate the frequency of this and BRIP1.2392C>T pathogenic variant in patients with breast cancer (BC) and/or EOC. A case-control study of 3767 cases and 2043 controls was undertaken investigating the presence of these variants using Sanger sequencing and gene panel data. Individuals with BC and/or EOC were grouped by family history. BRIP1 c.1045G>C was associated with increased risk of BC/EOC (OR = 37.7; 95% CI 5.3–444.2; P = 0.0001). The risk was highest for women with EOC (OR = 140.8; 95% CI 23.5–1723.0; P < 0.0001) and lower for BC (OR = 11.1; 95% CI 1.2–106.5; P = 0.1588). BRIP1 c.2392C>T was associated with smaller risks for BC/EOC (OR = 5.4; 95%CI 2.4–12.7; P = 0.0003), EOC (OR = 5.9; 95% CI 1.3–23.0; p = 0.0550) and BC (OR = 5.3; 95%CI 2.3–12.9; P = 0.0009). Our study highlights the importance of BRIP1 as an EOC susceptibility gene, especially in familial EOC. The variant BRIP1 c.1045G>C, rs149364097, is of particular interest as its dominant-negative effect may confer a higher risk of EOC than that of the previously reported BRIP1 c.2392C>T nonsense variant. Dominant-negative missense variants may confer higher risks than their loss-of-function counterparts.     

Association of MIR146A rs2910164 variation with a predisposition to sporadic breast cancer in a Pakistani cohort

Single‐nucleotide polymorphisms (SNPs) in genes coding for microRNAs (miRNAs) play a pivotal role in the progression of breast cancer (BC). We investigated the association of miR‐146a rs2910164 GC polymorphism with the risk of BC in the Pakistani population. The miR‐146a rs2910164 polymorphism was genotyped in 300 BC cases and 300 age‐ and gender‐matched healthy controls using T‐ARMS‐PCR. Genotype and allele frequencies were calculated and the association between genotypes and the risk of BC was calculated by odds ratio (OR) and confidence interval (95%). A significant difference in genotypic frequencies (χ² = 63.10; P = <0.0001) and allelic frequencies (OR = 0.3955 (0.3132–0.4993); P = < 0.0001) was observed between cases and controls. Furthermore, we also found that miR‐146 rs2910164 CC homozygote increased the risk of BC in the dominant (OR = 0.2397 (0.1629–0.3526); P = 0.0001; GG vs. GC + CC) and recessive (OR = 2.803 (1.865–4.213); P = <0.0001; CC vs. GC + GG) inheritance models. In summary, miR‐146a rs2910164 GC is significantly associated with BC in the Pakistani population. To our knowledge, this is the first study that assessed MIR146a rs2910164 G > C SNP in Pakistani population. By analyzing the secondary structure of MIR146A variant, a significant structural modification was noted. Study with a larger sample size is needed to further confirm of these findings.     

IFN‐γ +874T/A polymorphism increases susceptibility to post‐traumatic osteomyelitis

Immunological inflammatory reaction is one of the key links in the occurrence and development of post‐traumatic osteomyelitis after microbial invasion. Growing evidence suggests complex interactions between IFN‐γ and bone remodelling cells. However, potential association of IFN‐γ gene polymorphism with susceptibility to post‐traumatic osteomyelitis remains unclear. This study aimed to investigate the potential link between IFN‐γ +874T/A polymorphism and risk of developing post‐traumatic osteomyelitis. A total of 189 patients with post‐traumatic osteomyelitis and 200 healthy controls were enrolled for genotyping using the SNaPshot genotyping method. Statistically significant associations were found between the gene polymorphism and the risk of post‐traumatic osteomyelitis by dominant model (AA + AT vs. TT, OR = 1.820, p = .017) and heterozygous model (AT vs. TT, OR = 1.781, p = .029). Moreover, the frequency of mutant allele A was significantly higher in the patients than that in the healthy controls (15.07% vs. 9.25%, OR = 1.742, p = .013). IFN‐γ +874T/A polymorphism may contribute to the increased susceptibility to post‐traumatic osteomyelitis.     

Human leucocyte antigen‐G 14‐bp InDel polymorphism and oral squamous cell carcinoma risk in Chinese Han population: A case–control study

Human leucocyte antigen‐G (HLA‐G) is a nonclassical HLA class I molecule involved in tumour immune escape. The purpose of this study was to investigate the association between the 14‐bp insertion/deletion (InDel) polymorphism in the 3′ untranslated region (3′‐UTR) of HLA‐G gene and oral squamous cell carcinoma (OSCC) risk in Chinese Han population (216 cases and 193 healthy controls), and furthermore, to evaluate serum soluble HLA‐G (sHLA‐G) levels in the OSCC patients. Our results demonstrated that the Ins allele was significantly less frequent in the OSCC patients than that in the healthy controls (odds ratio [OR] = 0.75; 95% confidence interval [CI]: 0.57–0.99; p = 0.040). Distribution of the 14‐bp genotypes in the OSCC patients and the healthy controls revealed that the Ins/Ins genotype was associated with decreased OSCC risk in both the codominant model (Ins/Ins versus Del/Del; OR = 0.57; 95% CI = 0.33–0.99; p = 0.044) and the log‐additive model (OR = 0.76; 95% CI: 0.58–0.99; p = 0.044). The serum sHLA‐G level was significantly higher in the OSCC patients than those in the healthy controls (p < 0.001). Receiver operating characteristic (ROC) curve revealed the valuable diagnostic value of sHLA‐G for OSCC detection, with an area under the ROC curve (AUC) of 0.891 (95% CI: 0.856–0.925, p < 0.001). The OSCC patients with Ins/Ins genotype had lower serum sHLA‐G levels than those with Ins/Del and Del/Del genotypes (p = 0.015). Furthermore, serum sHLA‐G levels were significantly increased with the increasing TNM stages of the OSCC patients (p = 0.017). Our findings revealed that the HLA‐G 14‐bp InDel polymorphism might be a genetic risk factor for OSCC susceptibility, and the serum sHLA‐G may act as a promising biomarker for noninvasive diagnosis of OSCC.     

The association of CTLA‐4 A49G polymorphism with colorectal cancer risk in a Chinese Han population

Cytotoxic T‐lymphocyte antigen‐4 (CTLA‐4) is expressed in T cells and plays an important role in the regulation of T cell. CTLA‐4 has long been considered to be associated with various kinds of diseases. With the attempt to examine the association between CTLA‐4 A49G polymorphism and colorectal cancer risk in a Chinese Han population, we employed TaqMan assay to genotype the CTLA‐4 A49G polymorphism in 311 colorectal cancer cases and 389 cancer‐free controls. We found evidence of the association between CTLA‐4 A49G polymorphism and colorectal cancer risk (GG vs. AA: OR = 2.01, 95% CI = 1.29–3.07, P = 0.002; GA vs. AA: OR = 2.32, 95% CI = 1.53–3.57, P = 0.001; GA + GG vs. AA: OR = 2.16, 95% CI = 1.46–3.21, P = 0.001). Next, we performed a meta‐analysis to comprehensively examine the association between CTLA‐4 A49G polymorphism and colorectal cancer risk. We found a significant association between CTLA‐4 A49G polymorphism and colorectal cancer risk among Asians, which is consistent with our result. However, we found no evidence for the association between CTLA‐4 A49G polymorphism and colorectal cancer risk among Caucasians. In conclusion, we demonstrated that the CTLA‐4 A49G polymorphism increased the susceptibility of colorectal cancer in Asian population.     

Understanding the Genomic Structure of Copy‐Number Variation of the Low‐Affinity Fcγ Receptor Region Allows Confirmation of the Association of FCGR3B Deletion with Rheumatoid Arthritis

Fcγ receptors are a family of cell–surface receptors that are expressed by a host of different innate and adaptive immune cells, and mediate inflammatory responses by binding the Fc portion of immunoglobulin G. In humans, five low‐affinity receptors are encoded by the genes FCGR2A , FCGR2B , FCGR2C , FCGR3A , and FCGR3B , which are located in an 82.5‐kb segmental tandem duplication on chromosome 1q23.3, which shows extensive copy‐number variation (CNV). Deletions of FCGR3B have been suggested to increase the risk of inflammatory diseases such as systemic lupus erythematosus and rheumatoid arthritis (RA). In this study, we identify the deletion breakpoints of FCGR3B deletion alleles in the UK population and endogamous native American population, and show that some but not all alleles are likely to be identical‐by‐descent. We also localize a duplication breakpoint, confirming that the mechanism of CNV generation is nonallelic homologous recombination, and identify several alleles with gene conversion events using fosmid sequencing data. We use information on the structure of the deletion alleles to distinguish FCGR3B deletions from FCGR3A deletions in whole‐genome array comparative genomic hybridization (aCGH) data. Reanalysis of published aCGH data using this approach supports association of FCGR3B deletion with increased risk of RA in a large cohort of 1,982 cases and 3,271 controls (odds ratio 1.61, P = 2.9×10^?3).     

Analysis of PTPN22, ZFAT and MYO9B polymorphisms in Turner Syndrome and risk of autoimmune disease

Turner syndrome (TS) is one of the most common sexual chromosome abnormalities and is clearly associated with an increased risk of autoimmune diseases, particularly thyroid disease and coeliac disease (CD). Single‐nucleotide polymorphism analyses have been shown to provide correlative evidence that specific genes are associated with autoimmune disease. Our aim was to study the functional polymorphic variants of PTPN22 and ZFAT in relation to thyroid disease and those of MYO9B in relation to CD. A cross‐sectional comparative analysis was performed on Mexican mestizo patients with TS and age‐matched healthy females. Our data showed that PTPN22 C1858T (considered a risk variant) is not associated with TS (X² = 3.50, p = .61, and OR = 0.33 [95% CI = 0.10–1.10]). Also, ZFAT was not associated with TS (X² = 1.2, p = .28, and OR = 1.22 [95% CI = 0.84–1.79]). However, for the first time, rs2305767 MYO9B was revealed to have a strong association with TS (X² = 58.6, p = .0001, and OR = 10.44 [95% C = 5.51–19.80]), supporting a high level of predisposition to CD among TS patients. This report addresses additional data regarding the polymorphic variants associated with autoimmune disease, one of the most common complications in TS.     

ERAP1 variants are associated with ankylosing spondylitis in East Asian population: a new Chinese case–control study and meta‐analysis of published series

Endoplasmic reticulum aminopeptidase 1 (ERAP1) has been confirmed to be associated with ankylosing spondylitis (AS) in Caucasian. However, whether they are associated with AS in East Asian population remains unidentified. We investigated this relationship by a new Chinese case–control study and a meta‐analysis of published series. 368 cases and 460 controls were recruited in the Chinese case–control study. Genotyping was completed using the chip‐based matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Allelic associations were analysed using contingency tables. In the meta‐analysis, up to 2748 cases and 2774 controls from seven different studies and the new Chinese study were combined using Review Manager software version 5.1.1. Mantel–Haenszel or Inverse Variance test was used to calculate fixed or random‐effects pooled ORs. In the new Chinese study, strong association with AS was observed for marker rs10050860, rs27434 and rs1065407 at P value of <0.001. Moderate association was observed for rs30187 at P value of <0.01, while no association was observed for rs27044 (P = 0.37) and rs2287987 (P = 0.23). The meta‐analysis showed that rs27037 and rs30187 were strongly associated with AS (P < 0.00001). Significant association was also observed for rs27434 (P = 0.001). No association was shown for rs27044 (P = 0.70). We concluded that ERAP1 variants are associated with AS in East Asian population, indicating a common pathogenic mechanism for AS in East Asians and Caucasians.     

Association Between TNF‐α Promoter −308 A/G Polymorphism and Systemic Lupus Erythematosus Susceptibility: A Case–Control Study and Meta‐Analysis

The tumour necrosis factor‐α (TNF‐α) promoter −308 A/G polymorphism plays an important role in the aetiology of systemic lupus erythematosus (SLE). Several studies have estimated the association between TNF‐α −308 A/G and SLE risk. However, results were inconsistent. A case–control study was carried out to explore the association between TNF‐α −308 A/G and the SLE risk in a Chinese Han population. Meta‐analysis combining present with previous studies was conducted to further explore the association. Our case–control study included 556 patients with SLE along with 570 matched healthy controls. TNF‐α −308 A allele was significantly increased in patients with SLE compared with controls (OR = 2.184, 95% CI: 1.718–2.778, P < 0.001). Genotypes AA and AG were associated with the susceptibility to SLE as compared with the GG genotype, as well as the dominant model (AA+AG versus GG), respectively. The meta‐analysis included 41 comparative studies involving 4799 patients and 6635 controls. An association between SLE and allele A was found in the overall populations (OR = 1.70, 95% CI: 1.46–1.98, P < 0.001). In addition, we discussed the correlation between this polymorphism and lupus nephritis (LN) risk, showing that allele A was significantly related to LN in the overall populations (OR = 1.80, 95% CI: 1.21–2.68, P = 0.004). The results from our case–control study and the meta‐analysis indicate that the TNF‐α −308 A allele is significantly associated with an increased risk of SLE/LN.     

TAP1 and TAP2 gene polymorphism in rheumatoid arthritis in a population in eastern France

The ‘transporter associated with antigen processing’ (TAP) gene products are involved in the processing of endogenous peptides that bind to class I molecules. Polymorphism within these genes could alter the level of the immune response, a phenomenon relevant to the development of autoimmune diseases. In this study, we examined the polymorphism of TAP1 and TAP2 genes in patients with rheumatoid arthritis (RA). TAP1 and TAP2 typing was performed for 138 Caucasian RA patients and 100 healthy controls, all originating from eastern France. TAP1 polymorphic residues at positions 333 and 637 and amino acid variants 379, 565, 651 and 665 in the TAP2 gene were found using amplification refractory mutation system–polymerase chain reaction (ARMS‐PCR). This method enabled us to determine four TAP1 alleles (TAP1A to TAP1D) and eight TAP2 alleles (TAP2A to TAP2H). All patients and controls had been HLA‐DRB1* genotyped. The polymorphic residues TAP1³³³ and TAP1⁶³⁷ did not show any difference in their distribution between patients and controls. Similar findings were obtained for TAP2³⁷⁹ and TAP2⁶⁶⁵. However, we found an increased frequency of Thr homozygosity and heterozygosity at position 565 in the TAP2 gene in RA patients (RA vs. controls: 25.3 vs. 14%; P = 0.032; OR = 2.09; CI = 1.01–4.38). Similarly, the prevalence of subjects who were homozygote and heterozygote for Cys⁶⁵¹ was increased in the RA group (RA vs. controls: 36.8 vs. 11%; P = 0.02). The dimorphic site TAP2⁵⁶⁵ defines TAP2D and TAP2E alleles, while the site at position 651 characterizes TAP2F. Thus, we found that TAP2D and TAP2E alleles were more prevalent in RA, but not significantly so (RA vs. controls: TAP2D: 10 vs. 3.6%; P = 0.24; TAP2E: 3.6 vs. 0%; P = 0.19). Similarly, the frequency of TAP2F was higher in RA patients (24.5%) than in controls (11.3%), but this was not significant after correction (P = 0.029; P_corr = 0.17). Finally, we found no linkage disequilibrium between DRB1* RA‐associated alleles and amino acid substitution Thr⁵⁶⁵ or TAP2D and TAP2E alleles, whereas Cys⁶⁵¹ (and TAP2F) was not independent of DRB1*04, a strongly RA‐associated allele. Finally, Thr at position 565 in the TAP2 gene was associated with manifestations of disease severity in only a few patients. Examination of TAP1 and TAP2 gene polymorphisms in RA patients revealed an association between a particular amino acid residue, namely Thr⁵⁶⁵ in the TAP2 gene, and RA. This association was found to be weak and did not seem to be a predictor for the severity of the disease.     

Doubly Reactive INS‐IGF2 Autoantibodies in Children with Newly Diagnosed Autoimmune (type 1) Diabetes

The splice variant INS‐IGF2 entails the preproinsulin signal peptide, the insulin B‐chain, eight amino acids of the C‐peptide and 138 unique amino acids from an ORF in the IGF2 gene. The aim of this study was to determine whether levels of specific INS‐IGF2 autoantibodies (INS‐IGF2A) were related to age at diagnosis, islet autoantibodies, HLA‐DQ or both, in patients and controls with newly diagnosed type 1 diabetes. Patients (n = 676), 0–18 years of age, diagnosed with type 1 diabetes in 1996–2005 and controls (n = 363) were analysed for specific INS‐IGF2A after displacement with both cold insulin and INS‐IGF2 to correct for non‐specific binding and identify double reactive sera. GADA, IA‐2A, IAA, ICA, ZnT8RA, ZnT8WA, ZnT8QA and HLA‐DQ genotypes were also determined. The median level of specific INS‐IGF2A was higher in patients than in controls (P < 0.001). Irrespective of age at diagnosis, 19% (126/676) of the patients had INS‐IGF2A when the cut‐off was the 95th percentile of the controls (P < 0.001). The risk of INS‐IGF2A was increased among HLA‐DQ2/8 (OR = 1.509; 95th CI 1.011, 2.252; P = 0.045) but not in 2/2, 2/X, 8/8, 8/X or X/X (X is neither 2 nor 8) patients. The association with HLA‐DQ2/8 suggests that this autoantigen may be presented on HLA‐DQ trans‐heterodimers, rather than cis‐heterodimers. Autoantibodies reactive with both insulin and INS‐IGF2A at diagnosis support the notion that INS‐IGF2 autoimmunity contributes to type 1 diabetes.     

High‐Resolution Survey in Familial Parkinson Disease Genes Reveals Multiple Independent Copy Number Variation Events in PARK2

A high density comparative genomic hybridization array was designed to evaluate CNVs in the genomic region of six familial PD genes in 181 PD cases and 67 controls. No CNV was found in PARK7, ATP13A2, PINK1, and LRRK2. Intronic‐only CNVs were found in SNCA and PARK2 but were not associated with PD risk. A whole‐gene duplication of SNCA was found in one case. The allele frequency of PARK2 exonic CNV is significantly higher in cases than in controls (P = 0.02), higher in early‐onset (AAO ≤ 40) than in late‐onset cases (P = 0.001), and higher in familial than in sporadic cases (P = 0.005). Except for single exon 2 duplications, all PARK2 exonic CNVs have different breakpoints, even when the same exon(s) were involved. In conclusion, except for SNCA and PARK2, CNVs are not a major contributing mechanism for the familial PD genes examined. The majority of PARK2 exonic CNVs are not recurrent.